#$ -S /bin/bash
#$ -t 1-86
#$ -o /home/srlab/Documents/DNR_PECAN_Run_1_20170303_Output/pecan/log
#$ -e /home/srlab/Documents/DNR_PECAN_Run_1_20170303_Output/pecan/log
#$ -wd /home/srlab/Documents/DNR_PECAN_Run_1_20170303_Output/pecan

date
MZML=/home/srlab/Documents/DNR_PECAN_Run_1_20170303/2017_January_23_envtstress_oyster5.mzML
ISOWINDOW=`awk "NR==$SGE_TASK_ID" /home/srlab/Documents/DNR_PECAN_Run_1_20170303_Output/isolationScheme.txt`

## to output the version info
echo "/home/shared/pecan/bin/pecan -b /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt --minCharge 2 --maxCharge 3 --ionTypes y $MZML /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt $ISOWINDOW 2017_January_23_envtstress_oyster5"
/home/shared/pecan/bin/pecan -b /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt --minCharge 2 --maxCharge 3 --ionTypes y $MZML /home/srlab/Documents/DNR_PECAN_Run_1_20170303/Combined-gigas-QC.txt $ISOWINDOW 2017_January_23_envtstress_oyster5 
echo 'Job complete!'